Mechanisms linking diversity, productivity and invasibility in experimental bacterial communities

The interactive effects of parasites, disturbance, and productivity on experimental adaptive radiations

Disturbance, productivity, and natural enemies are significant determinants of the evolution of diversity, but their interactive effect remains unresolved. We develop a simple, qualitative model assuming trade-offs between growth rate, competitive ability and parasite resistance, to address the interactive effects of these variables on the evolution of host diversity. Consistent with previous studies our model predicts maximum diversity at intermediate levels of disturbance and productivity in the absence of parasitism. However, parasites break down these unimodal diversity relationships with productivity and disturbance, as selection for parasite resistance reduces the importance of growth rate-competitive ability trade-offs. We tested these predictions using the bacterium Pseudomonas fluorescens, which undergoes an adaptive radiation into spatial niche specialists under laboratory conditions. This is the first study of adaptive radiation in response to experimental manipulation of the three-way interaction between productivity, disturbance, and natural enemies. As hypothesized, unimodal diversity relationships with disturbance and productivity were weakened or disappeared in the presence of parasitic phages. This was the result of phages increasing diversity at environmental extremes, by imposing selection for phage-resistant variants, but decreasing diversity in less stressful environments, probably through reductions in resource competition. Phages had a net effect of increasing host diversity. Parasites and other natural enemies are therefore likely to have a large effect in mitigating the influence of other environmental variables on the evolution and maintenance of diversity.

Population bottlenecks promote cooperation in bacterial biofilms

Population bottlenecks are assumed to play a key role in the maintenance of social traits in microbes. Ecological parameters such as colonisation or disturbances can favour cooperation through causing population bottlenecks that enhance genetic structuring (relatedness). However, the size of the population bottleneck is likely to play a crucial role in determining the success of cooperation. Relatedness is likely to increase with decreasing bottleneck size thus favouring the evolution of cooperation. I used an experimental evolution approach to test this prediction with biofilm formation by the bacterium Pseudomonas fluorescens as the cooperative trait. Replicate populations were exposed to disturbance events every four days under one of six population bottleneck treatments (from 10³ to 10⁸ bacterial cells). In line with predictions, the frequency of evolved cheats within the populations increased with increasing bottleneck size. This result highlights the importance of ecologically mediated population bottlenecks in the maintenance of social traits in microbes.

NEGATIVE SELECTION EFFECTS SUPPRESS RELATIONSHIPS BETWEEN BACTERIAL DIVERSITY AND ECOSYSTEM FUNCTIONING

I assembled bacterial communities to explore the effects of bacterial diversity on multiple ecosystem functions, including bacterial community biovolume, decomposition of particulate organic matter, and biomass transfer to the next trophic level. The experiment used a two-way factorial design with four levels of bacterial diversity (one to four species) and the absence/presence of a bacterivorous ciliated protist Tetrahymena pyriformis as two main factors, and all possible combinations of the four bacterial taxa nested within each diversity level. Bacterial community biovolume increased as bacterial diversity increased, a result due largely to positive selection effects. Decomposition and consumer abundance, however, were unaffected by bacterial diversity, though both varied among bacterial composition treatments. Negative selection effects, the dominance of species that do not contribute significantly to ecosystem functioning, accounted for the lack of diversity effects on decomposition and consumer abundance. The presence of Tetrahymena reduced bacterial community biovolume but increased decomposition, without altering the diversity-functioning relationships. Decomposition was strongly linked with consumer abundance such that communities supporting larger consumer biomass exhibited higher decomposition rates. This study suggests that if the negative selection effect is common, as it might be when examining ecosystem variables other than biomass (due to the presence of keystone species that can contribute disproportionably to ecosystem functioning relative to their abundances), basic bacteria-mediated ecosystem processes, such as decomposition and energy transfer to the next trophic level, may not increase with bacterial diversity.

Cooperation Peaks at Intermediate Disturbance

Explaining cooperation is a challenge for evolutionary biology. Surprisingly, the role of extrinsic ecological parameters remains largely unconsidered. Disturbances are widespread in nature and have evolutionary consequences. We develop a mathematical model predicting that cooperative traits most readily evolve at intermediate disturbance. Under infrequent disturbance, cooperation breaks down through the accumulation of evolved cheats. Higher rates of disturbance prevent this because the resulting bottlenecks increase genetic structuring (relatedness) promoting kin selection for cooperation. However, cooperation cannot be sustained under very frequent disturbance if population density remains below the level required for successful cooperation. We tested these predictions by using cooperative biofilm formation by the bacterium Pseudomonas fluorescens. The proportion of biofilm-forming bacteria peaked at intermediate disturbance, in a manner consistent with model predictions. Under infrequent and intermediate disturbance, most bacteria occupied the biofilm, but the proportion of cheats was higher under less frequent disturbance. Under frequent disturbance, many bacteria did not occupy the biofilm, suggesting that biofilm dwelling was not as beneficial under frequent versus intermediate disturbance. Given the ubiquity of disturbances in nature, these results suggest that they may play a major role in the evolution of social traits in microbes.

Niche occupation limits adaptive radiation in experimental microcosms

Adaptive radiations have played a key role in the evolution of biological diversity. The breadth of adaptive radiation in an invading lineage is likely to be influenced by the availability of ecological niches, which will be determined to some extent by the diversity of the resident community. High resident diversity may result in existing ecological niches being filled, inhibiting subsequent adaptive radiation. Conversely, high resident diversity could result in the creation of novel ecological niches or an increase in within niche competition driving niche partitioning, thus promoting subsequent diversification. We tested the role of resident diversity on adaptive radiations in experimental populations of the bacterium Pseudomonas fluorescens that readily diversify into a range of niche specialists when grown in a heterogeneous environment. We allowed an undiversified strain to invade resident communities that varied in the number of niche specialists. The breadth of adaptive radiation attainable by an invading lineage decreased with increasing niche occupation of the resident community. Our results highlight the importance of niche occupation as a constraint on adaptive radiation.

Ecology of microbial invasions: amplification allows virus carriers to invade more rapidly when rare

Locally adapted residents present a formidable barrier to invasion . One solution for invaders is to kill residents . Here, we explore the comparative ecological dynamics of two distinct microbial mechanisms of killing competitors, via the release of chemicals (e.g., bacteriocins ) and via the release of parasites (e.g., temperate phage ). We compared the short-term population dynamics of susceptible E. coli K12 and isogenic carriers of phage varphi80 in experimental cultures to that anticipated by mathematical models using independently derived experimental parameters. Whereas phages are a direct burden to their carriers because of probabilistic host lysis, by killing competitor bacteria they can indirectly benefit bacterial kin made immune by carrying isogenic phage. This is similar to previously described bacteriocin-mediated effects. However, unlike chemical killing, viable phage trigger an epidemic among susceptible competitors, which become factories producing more phage. Amplification makes phage carriers able to invade well-mixed susceptibles even faster when rare, whereas chemical killers can only win in a well-mixed environment when sufficiently abundant. We demonstrate that for plausible parameters, the release of chemical toxins is superior as a resident strategy to repel invasions, whereas the release of temperate phage is superior as a strategy of invasion.

Character displacement promotes cooperation in bacterial biofilms

Resource competition within a group of cooperators is expected to decrease selection for cooperative behavior but can also result in diversifying selection for the use of different resources, which in turn could retard the breakdown of cooperation. Diverse groups are likely to be less susceptible to invasion by noncooperating social cheats: First, competition repression resulting from character displacement may provide less of a selective advantage to cheating; second, cheats may trade off the ability to exploit cooperators that specialize in one type of resource against cooperators that specialize in another ; third, diverse communities of any kind may have higher invasion resistance because there are fewer resources available for an invader to use . Furthermore, diverse groups are likely to be more productive than clonal groups if a wider range of total resources are being used . We addressed these issues by using the cooperative trait of biofilm formation in Pseudomonas fluorescens. Character displacement through resource competition evolved within biofilms; productivity increased with increasing character displacement, and diverse biofilms were less susceptible to invasion by cheats. These results demonstrate that diversification into different ecological niches can minimize selection against cooperation in the face of local resource competition.

Adaptive radiation in microbial microcosms

It has often been argued that evolutionary diversification is the result of divergent natural selection for specialization on alternative resources. I provide a comprehensive review of experiments that examine the ecology and genetics of resource specialization and adaptive radiation in microbial microcosms. In these experiments, resource heterogeneity generates divergent selection for specialization on alternative resources. At a molecular level, the evolution of specialization is generally attributable to mutations that de-regulate the expression of existing biosynthetic and catabolic pathways. Trade-offs are associated with the evolution of resource specialization, but these trade-offs are often not the result of antagonistic pleiotropy. Replicate adaptive radiations result in the evolution of a similar assemblage of specialists, but the genetic basis of specialization differs in replicate radiations. The implications of microbial selection experiments for evolutionary theory are discussed and future directions of research are proposed.

Host ecology determines the relative fitness of virus genotypes in mixed-genotype nucleopolyhedrovirus infections

Mixed-genotype infections are common in many natural host-parasite interactions. Classical kin-selection models predict that single-genotype infections can exploit host resources prudently to maximize fitness, but that selection favours rapid exploitation when co-infecting genotypes share limited host resources. However, theory has outpaced evidence: we require empirical studies of pathogen genotypes that naturally co-infect hosts. Do genotypes actually compete within hosts? Can host ecology affect the outcome of co-infection? We posed both questions by comparing traits of infections in which two baculovirus genotypes were fed to hosts alongside inocula of the same or a different genotype. The host, Panolis flammea, is a herbivore of Pinus sylvestris and Pi. contorta. The pathogen, PfNPV (a nucleopolyhedrovirus), occurs naturally as mixtures of genotypes that differ, when isolated, in pathogenicity, speed of kill and yield. Single-genotype infection traits failed to predict the 'winning' genotypes in co-infections. Co-infections infected and caused lethal disease in more hosts, and produced high yields, relative to single-genotype infections. The need to share with nonkin did not cause fitness costs to either genotype. In fact, in hosts feeding on Pi. sylvestris, one genotype gained increased yields in mixed-genotype infections. These results are discussed in relation to theory surrounding adaptive responses to competition with nonkin for limited resources.

An ecological perspective on bacterial biodiversity

Bacteria may be one of the most abundant and species-rich groups of organisms, and they mediate many critical ecosystem processes. Despite the ecological importance of bacteria, past practical and theoretical constraints have limited our ability to document patterns of bacterial diversity and to understand the processes that determine these patterns. However, recent advances in molecular techniques that allow more thorough detection of bacteria in nature have made it possible to examine such patterns and processes. Here, we review recent studies of the distribution of free-living bacterial diversity and compare our current understanding with what is known about patterns in plant and animal diversity. From these recent studies a preliminary picture is emerging: bacterial diversity may exhibit regular patterns, and in some cases these patterns may be qualitatively similar to those observed for plants and animals.